LCB has created plugins for BASE and the LCB Datawarehouse.
Since it is based on open-source code, the product is open-source as well.
Note that the code requires a recent installation of BASE and other
software as described in the included README file.
They are NOT meant to be run as stand-alone applications.

Plug-in:plugins.tar.gz (28k)Date: 2005-11-14Version: 4.01Creator: Adam AmeurSupport: LCBDWH TeamDescription: Please see all the details in the README and change.log
files provided within this plug-in distribution.

Plug-in:R-plugins_lcb_v1.01.tar.gz (13k)Date: 2004-03-17Version: 1.01Creator:Ola SpjuthSupport: LCBDWH TeamDescription: Please see all the details in the readme.txt and change.log
files provided within this plug-in distribution.

R: Normalization between arrays
Normalization between arrays (scaling) using R functions from Bioconductor(LIMMA).

R: B-statistics
Calculates B-statistics, t-statistics, and p-value for ranking genes
Produces graphs and a ranked list of reporters based on B-statistics using Bioconductor(LIMMA)and SMA.
Features plots: QQT plot, B-stat plot with geneNames, B-stat plot with reporterID

R: B-statistics with dupcor
Calculates B-statistics, t-statistics, and p-value for ranking genes with correction of duplicates (dupcor)
Produces graphs and a ranked list of reporters based on B-statistics using Bioconductor(LIMMA)and SMA.
Features plots: QQT plot, B-stat plot with geneNames, B-stat plot with reporterID

Files included

Description

base_R.pl

Perl-script for executing R-scripts from BASE

parse.basefile.R

Functions for reading/writing BASEfiles within R

arrayplots.R

R-script for constructing various Array plots

rnorm.R

R-script using Bioconductor(LIMMA) functions to normalize 2ch arrays

rnorm.betw.arr.R

R-script using Bioconductor(LIMMA) functions to normalize between arrays

bstat.R

R-script using Bioconductor(LIMMA) functions to rank genes by B-statistics

bstat.dupcor.R

R-script using Bioconductor(LIMMA) functions to rank genes by B-statistics with duplicate correction (dupcor)